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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.911704570237638,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C158_adrenal_gastric_temporal_parietal_duodenum_caudate_putamen
|full_id=C158_adrenal_gastric_temporal_parietal_duodenum_caudate_putamen
|gostat_on_coexpression_clusters=GO:0042720!mitochondrial inner membrane peptidase complex!0.0130478988412968!83943$GO:0004244!mitochondrial inner membrane peptidase activity!0.0130478988412968!83943$GO:0050954!sensory perception of mechanical stimulus!0.0130478988412968!152137;10253$GO:0007605!sensory perception of sound!0.0130478988412968!152137;10253$GO:0006627!mitochondrial protein processing!0.0138454744697207!83943$GO:0004237!membrane dipeptidase activity!0.0230717153481549!64180
|gostat_on_coexpression_clusters=GO:0042720!mitochondrial inner membrane peptidase complex!0.0130478988412968!83943$GO:0004244!mitochondrial inner membrane peptidase activity!0.0130478988412968!83943$GO:0050954!sensory perception of mechanical stimulus!0.0130478988412968!152137;10253$GO:0007605!sensory perception of sound!0.0130478988412968!152137;10253$GO:0006627!mitochondrial protein processing!0.0138454744697207!83943$GO:0004237!membrane dipeptidase activity!0.0230717153481549!64180

Revision as of 14:10, 12 September 2012


Full id: C158_adrenal_gastric_temporal_parietal_duodenum_caudate_putamen



Phase1 CAGE Peaks

Hg19::chr10:10836699..10836711,-p10@SFTA1P
Hg19::chr10:10836739..10836753,-p8@SFTA1P
Hg19::chr10:36988176..36988178,-p@chr10:36988176..36988178
-
Hg19::chr10:37004821..37004852,-p@chr10:37004821..37004852
-
Hg19::chr10:90305239..90305251,-p10@RNLS
Hg19::chr12:78227833..78227840,-p@chr12:78227833..78227840
-
Hg19::chr12:86272170..86272176,+p@chr12:86272170..86272176
+
Hg19::chr12:91218399..91218404,+p@chr12:91218399..91218404
+
Hg19::chr13:67730380..67730387,+p@chr13:67730380..67730387
+
Hg19::chr13:69251442..69251477,+p@chr13:69251442..69251477
+
Hg19::chr13:69259745..69259757,-p@chr13:69259745..69259757
-
Hg19::chr13:80914790..80914795,-p41@SPRY2
Hg19::chr13:90020369..90020372,-p@chr13:90020369..90020372
-
Hg19::chr14:47289600..47289605,-p@chr14:47289600..47289605
-
Hg19::chr14:47289641..47289643,-p@chr14:47289641..47289643
-
Hg19::chr14:47289644..47289662,-p@chr14:47289644..47289662
-
Hg19::chr14:85978533..85978538,-p@chr14:85978533..85978538
-
Hg19::chr15:36251080..36251084,-p@chr15:36251080..36251084
-
Hg19::chr16:16593388..16593394,+p@chr16:16593388..16593394
+
Hg19::chr16:68014345..68014352,-p1@AB590471
Hg19::chr16:68014358..68014363,-p3@DPEP3
Hg19::chr16:68014368..68014384,-p2@DPEP3
Hg19::chr16:68014387..68014423,-p1@DPEP3
Hg19::chr19:14444525..14444559,+p1@uc002myk.2
Hg19::chr1:218214846..218214850,-p@chr1:218214846..218214850
-
Hg19::chr1:218221538..218221546,-p@chr1:218221538..218221546
-
Hg19::chr1:218222265..218222274,-p@chr1:218222265..218222274
-
Hg19::chr1:218388686..218388689,-p@chr1:218388686..218388689
-
Hg19::chr1:82934455..82934461,-p@chr1:82934455..82934461
-
Hg19::chr1:82951436..82951474,-p@chr1:82951436..82951474
-
Hg19::chr1:84326618..84326622,-p1@ENST00000417565
Hg19::chr21:21703199..21703203,-p@chr21:21703199..21703203
-
Hg19::chr21:21823911..21823933,+p@chr21:21823911..21823933
+
Hg19::chr21:23058648..23058654,-p1@ENST00000416182
Hg19::chr21:23066072..23066082,+p@chr21:23066072..23066082
+
Hg19::chr21:23066147..23066153,+p@chr21:23066147..23066153
+
Hg19::chr21:23120868..23120880,+p@chr21:23120868..23120880
+
Hg19::chr21:23650444..23650446,+p@chr21:23650444..23650446
+
Hg19::chr2:132300828..132300841,-p1@uc002ttc.1
Hg19::chr2:150961763..150961789,-p@chr2:150961763..150961789
-
Hg19::chr2:150961910..150961916,-p@chr2:150961910..150961916
-
Hg19::chr2:150969651..150969663,+p@chr2:150969651..150969663
+
Hg19::chr2:150969704..150969713,+p@chr2:150969704..150969713
+
Hg19::chr2:150969742..150969756,+p@chr2:150969742..150969756
+
Hg19::chr2:150978421..150978425,+p@chr2:150978421..150978425
+
Hg19::chr2:187685152..187685168,-p@chr2:187685152..187685168
-
Hg19::chr2:187685199..187685210,-p@chr2:187685199..187685210
-
Hg19::chr2:77315799..77315830,+p@chr2:77315799..77315830
+
Hg19::chr3:146962974..146962979,-p@chr3:146962974..146962979
-
Hg19::chr3:147450214..147450243,-p@chr3:147450214..147450243
-
Hg19::chr3:147869637..147869641,+p@chr3:147869637..147869641
+
Hg19::chr3:161200616..161200619,+p@chr3:161200616..161200619
+
Hg19::chr3:174950074..174950087,-p@chr3:174950074..174950087
-
Hg19::chr3:174950099..174950115,-p@chr3:174950099..174950115
-
Hg19::chr3:175131802..175131807,-p@chr3:175131802..175131807
-
Hg19::chr3:181328302..181328339,+p4@SOX2-OT
Hg19::chr3:181328346..181328351,+p22@SOX2-OT
Hg19::chr3:181328363..181328382,+p5@SOX2-OT
Hg19::chr3:181328387..181328399,+p16@SOX2-OT
Hg19::chr3:181328459..181328465,+p27@SOX2-OT
Hg19::chr3:181328472..181328478,+p25@SOX2-OT
Hg19::chr3:181328499..181328502,+p32@SOX2-OT
Hg19::chr3:190580437..190580450,-p1@GMNC
Hg19::chr3:190580477..190580489,-p2@GMNC
Hg19::chr3:190999899..190999913,-p10@UTS2D
Hg19::chr3:190999916..190999925,-p13@UTS2D
Hg19::chr3:190999951..190999959,-p15@UTS2D
Hg19::chr3:191000039..191000046,-p9@UTS2D
Hg19::chr3:191047287..191047298,+p11@CCDC50
Hg19::chr3:85553584..85553599,-p@chr3:85553584..85553599
-
Hg19::chr3:85553737..85553767,+p1@AB646740
p1@AB646741
p1@AB646742
p1@AB646743
Hg19::chr4:34336968..34336974,-p@chr4:34336968..34336974
-
Hg19::chr4:34480309..34480321,-p@chr4:34480309..34480321
-
Hg19::chr4:35102522..35102546,+p@chr4:35102522..35102546
+
Hg19::chr4:35107931..35107966,+p@chr4:35107931..35107966
+
Hg19::chr4:67618078..67618083,-p@chr4:67618078..67618083
-
Hg19::chr4:67651552..67651563,+p@chr4:67651552..67651563
+
Hg19::chr5:103573467..103573478,+p@chr5:103573467..103573478
+
Hg19::chr5:103625303..103625326,+p@chr5:103625303..103625326
+
Hg19::chr5:28339690..28339727,-p@chr5:28339690..28339727
-
Hg19::chr5:92020578..92020613,-p@chr5:92020578..92020613
-
Hg19::chr5:92023982..92024005,-p4@ENST00000503489
Hg19::chr5:92024011..92024031,-p3@ENST00000503489
Hg19::chr5:92179437..92179443,+p@chr5:92179437..92179443
+
Hg19::chr6:113369869..113369877,+p@chr6:113369869..113369877
+
Hg19::chr6:113454693..113454704,+p@chr6:113454693..113454704
+
Hg19::chr6:122216918..122216922,-p@chr6:122216918..122216922
-
Hg19::chr6:122409629..122409642,-p@chr6:122409629..122409642
-
Hg19::chr6:94129263..94129284,-p1@EPHA7
Hg19::chr6:94129519..94129544,+p@chr6:94129519..94129544
+
Hg19::chr6:94845210..94845215,+p@chr6:94845210..94845215
+
Hg19::chr7:111033178..111033202,-p11@IMMP2L
Hg19::chr7:111051726..111051739,-p@chr7:111051726..111051739
-
Hg19::chr7:111051766..111051788,-p@chr7:111051766..111051788
-
Hg19::chr7:111051794..111051815,-p@chr7:111051794..111051815
-
Hg19::chr7:111051818..111051822,-p@chr7:111051818..111051822
-
Hg19::chr7:111054273..111054319,-p@chr7:111054273..111054319
-
Hg19::chr7:15802479..15802491,+p@chr7:15802479..15802491
+
Hg19::chr7:15802505..15802513,+p@chr7:15802505..15802513
+
Hg19::chr7:80824380..80824393,+p@chr7:80824380..80824393
+
Hg19::chr8:115584851..115584862,+p@chr8:115584851..115584862
+
Hg19::chr8:115584867..115584882,+p@chr8:115584867..115584882
+
Hg19::chr8:130152310..130152315,+p@chr8:130152310..130152315
+
Hg19::chr8:59953375..59953393,-p@chr8:59953375..59953393
-
Hg19::chr9:13323362..13323373,-p1@ENST00000433817
Hg19::chr9:30925323..30925363,-p@chr9:30925323..30925363
-
Hg19::chrX:13062752..13062771,-p2@FAM9C
Hg19::chrX:134975753..134975758,+p2@SAGE1
Hg19::chrX:2291152..2291163,-p@chrX:2291152..2291163
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0042720mitochondrial inner membrane peptidase complex0.0130478988412968
GO:0004244mitochondrial inner membrane peptidase activity0.0130478988412968
GO:0050954sensory perception of mechanical stimulus0.0130478988412968
GO:0007605sensory perception of sound0.0130478988412968
GO:0006627mitochondrial protein processing0.0138454744697207
GO:0004237membrane dipeptidase activity0.0230717153481549



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.48e-3594
nervous system3.48e-3594
central nervous system1.11e-3482
neural tube5.73e-3057
neural rod5.73e-3057
future spinal cord5.73e-3057
neural keel5.73e-3057
regional part of brain1.53e-2959
brain6.33e-2869
future brain6.33e-2869
adult organism8.85e-27115
regional part of forebrain2.23e-2341
forebrain2.23e-2341
future forebrain2.23e-2341
anterior neural tube3.82e-2342
neural plate4.98e-2386
presumptive neural plate4.98e-2386
neurectoderm2.48e-2290
telencephalon7.38e-2034
gray matter7.57e-2034
brain grey matter7.57e-2034
regional part of telencephalon2.55e-1933
cerebral hemisphere1.06e-1832
ectoderm-derived structure3.82e-18169
ectoderm5.95e-18173
presumptive ectoderm5.95e-18173
pre-chordal neural plate1.96e-1561
cerebral cortex1.43e-1425
pallium1.43e-1425
head2.63e-13123
regional part of cerebral cortex8.15e-1322
anterior region of body8.25e-13129
craniocervical region8.25e-13129
multi-tissue structure6.91e-12347
neocortex9.49e-1220
tube1.57e-10194
organism subdivision1.01e-09365
embryo1.08e-09612
anatomical cluster4.17e-09286
anatomical conduit5.24e-09241
cell layer2.70e-08312
multi-cellular organism3.25e-08659
posterior neural tube5.82e-0815
chordal neural plate5.82e-0815
epithelium6.34e-08309
embryonic structure1.26e-07605
developing anatomical structure1.26e-07605
germ layer2.04e-07604
embryonic tissue2.04e-07604
presumptive structure2.04e-07604
epiblast (generic)2.04e-07604
nucleus of brain9.29e-079
neural nucleus9.29e-079


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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